The sprint was delayed due to wet conditions following a spell of torrential rain earlier in the day but apart from a few damp patches on the track, dry conditions greeted the riders with the sun low on the horizon.
VR46 Racing's Bezzecchi had not put a foot wrong to claim his third pole of the season but following a poor start, he crashed on the first corner when he was clipped by his teammate Luca Marini (26).
Martin started second on the grid but he had a perfect launch to take the lead going into the first corner ahead of Bagnaia and the two Hondas of Marc Marquez (30) and Joan Mir (26).
Mir had looked good in qualifying but he made a mistake on turn three after three laps and lost his balance, allowing Brad Binder in the Red Bull KTM to move up to fourth and pressure Marquez for the final podium position.
Bezzecchi managed to rejoin the race and the Italian was a man on a mission as he worked his way up the grid, setting multiple fastest laps. But with only 11 laps in the sprint, he ran out of time but still managed to finish a creditable fifth.
With Martin and Bagnaia cruising, the biggest battle on the final laps was Marquez keeping Binder at bay for third place and it was the Spaniard who eventually came out on top for just his second sprint podium of the season.
"This year has been very difficult," Marquez said. "I'm super happy, I know that in a single lap I was fast but always behind somebody. Pecco (Bagnaia) was very far."
The result leaves Bagnaia on 292 points in the riders championship, 33 points ahead of Martin, while Bezzecchi fell 69 points behind the reigning champion.
"We were just very lucky the conditions were better in the sprint," Bagnaia said.
"I had a good race for the situation we're in. Finishing second was the maximum and we have to be happy with it."
